LANCL1 p.Arg41=
c.121C>A · rs116046523 · VCV783351
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.24%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.28 | acceptor loss · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP -2.5, phastCons 1 |
| Overall | ||
| CADD | 10.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.24%
African / African-American · 2,430/74,996 alleles
Filtering AF
3.13%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.09%
Overall
0.17%
2,737/1,614,036 alleles · low-frequency
exomes 1,356/1,461,804 · genomes 1,381/152,232 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.24% | 31 |
| Remaining individualsnot grpmax-eligible | 0.238% | 419 |
| Admixed American | 0.195% | 513 |
| Middle Eastern | 0.066% | 1,516 |
| European (non-Finnish) | 0.00297% | 33,714 |
| South Asian | 0.0022% | 45,535 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- LANCL1
- Protein
- p.Arg41=
- Coding
- c.121C>A
- MANE Select
- NM_006055
- dbSNP
- rs116046523
- Type
- single nucleotide variant
- Location
- chr2:210472037 (GRCh38)
- Gene constraint
- LOEUF 1.304 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.52 · 6 PDB
- Residue 41
- an α-helix
Similar variants
- LANCL1 p.Ala115Val Uncertain significance ★ ⚠ same type
- LANCL1 p.Ala117Thr Uncertain significance ★ ⚠ same type
- LANCL1 p.Ala118Thr Uncertain significance ★ ⚠ same type
- LANCL1 p.Ala147Asp Uncertain significance ★ ⚠ same type
- LANCL1 p.Ala18Val Uncertain significance ★ ⚠ same type
- LANCL1 p.Ala222Thr Uncertain significance ★ ⚠ same type
- LANCL1 p.Ala279Ser Uncertain significance ★ ⚠ same type
- LANCL1 p.Ala279Thr Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/lancl1-p-arg41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown